I already gave you the way in AlliedModders, but maybe this will help people here too.
read carefully because it's detailed, and it worked for me perfectly

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after running the waypoints menu correctly, do the following:
- activate the waypoints display and auto-waypointing features, in the options menu.
- browse your map, don't leave any empty location.
- make the specific waypoints like: ladder, camp, and jump, etc. manually (the jump has two attached waypoints, if no then you need to retry it).
- you don't need to make all the kinds of waypoints, like the "camp no-hostage" in de_ maps, etc.
- check your work, generally there are some areas which aren't connected to the whole waypoints web.
- save everytime, even if having errors until you finish.
- when testing, you may need the "podbot menu" to fill the server, kick the bots, etc.
and never forget, that making easy binds will help you a lot.
Credit: KWo who showed me how to make waypoints.